Entry: NAFlex_TCGAhmet


Nucleic Acid Data:


SequenceCGCGTXGACGCG
Rev. SequenceCGCGTXGACGCG
TypeDNA
SubTypeB
Chainsduplex
Pdb-
LigandsNo
KeywordsDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral


Simulation Metadata
Force FieldparmBSC1
Simulation Date2015-Apr-26
Simulated Time500 ns
Time Step1ps
PartsDNA+ions
Temperature298K
WaterTIP3P
Additional SolventNo
Counter IonsNa+
Ionic ConcentrationElectroneutrality
Additional IonsNo
Additional MoleculesNo
Ions ParametersDang
Unified Molecular Modeling (UMM) Metadata
(Click to see full UMM)
Simulation Metadata (UMM)
AdditionalIonsNo
AdditionalMoleculesNo
AdditionalSolventNo
AuthorP.D.
Chainsduplex
Commentsonly last 250 ns (so 250000 frames out of 500000)
CounterIonsNa+
Formatmdcrd
FrameStep1ps
Frames500000
IonicConcentrationElectroneutrality
IonsParametersDang
LigandsNo
NucTypeDNA
PDBNONE
PartsDNA+ions
RMSd_avg1.779
RMSd_stdev0.307
Rgyr_avg13.210
Rgyr_stdev0.264
SASA_avg4406.721
SASA_stdev71.718
SubTypeB
Temperature298K
TopologyTCGAhmet_nowat.prmtp
TrajectoryTCGAhmet_last250ns_nowatReimg.mdcrd
WaterTIP3P
_idNAFlex_TCGAhmet
authorsIvan Ivani, Pablo D. Dans, Agnès Noy, Alberto Pérez, Ignacio Faustino, Adam Hospital, Jürgen Walther, Pau Andrio, Ramon Goñi, Alexandra Balaceanu, Guillem Portella, Federica Battistini, Josep Lluís Gelpí, Carlos González, Michele Vendruscolo, Charles A. Laughton, Sarah A. Harris, David A. Case and Modesto Orozco
datasetArray
date2015-Apr-26
descriptionDNA-B Duplex Naked ParmBSC1 TIP3P Electroneutral
forceFieldparmBSC1
ionsModel-
moleculeTypeDna
rev_sequenceCGCGTXGACGCG
saltConcentration-
sequenceCGCGTXGACGCG
soluteAtoms764
soluteCharge-22
soluteResidues24
solventAtoms-
solventResidues-
time500
totalAtoms764
totalCharge-22
totalIons-
totalResidues24
Quality Control
RMSd-
Rgyr-
SASA-
RMSf-